COBREXA 2: tidy and scalable construction of complex metabolic models#

Authors#

Miroslav Kratochvil, St. Elmo Wilken, Oliver Ebenhöh, Reinhard Schneider, Venkata Pardhasaradhi Satagopam

Abstract#

Constraint-based metabolic models offer a scalable framework to investigate biological systems using optimality principles. Construction and simulation of detailed models that utilize multiple kinds of constraint systems poses a significant coding overhead, complicating implementation of new types of analyses. We present an improved version of the constraint-based metabolic modeling package COBREXA, which utilizes a hierarchical model construction framework that decouples the implemented analysis algorithms into independent, yet re-combinable, building blocks. By removing the need to re-implement modeling components, assembly of complex metabolic models is simplified, which we demonstrate on use-cases of resource-balanced models, and enzyme-constrained flux balance models of interacting bacterial communities. Notably, these models show improved predictive capabilities in both monoculture and community settings. In perspective, the re-usable model-building components in COBREXA 2 provide a sustainable way to handle increasingly complex models in constraint-based modeling.